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Mykrobe-tools / mykrobe

Antibiotic resistance prediction in minutes
MIT License
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Using of Mykrobe tool for targeted next generation sequencing #182

Closed afsanarupa closed 6 days ago

afsanarupa commented 7 months ago

Dear All, Can I use Mykrobe tool for targeted sequencing instead of whole genome sequencing?

iqbal-lab commented 6 months ago

Apologies for missing this. I assume you mean targeted whete the targets are amplicons over AMR genes, as it done for m tuberculosis.

We looked into this recently with a colleague. Normally mykrobe will refuse to make predictions unless it can confirm the species first. You can force mykrobe to ignore the speciation step. But it still expects the same average depth across the whole genome . If you map your reads first, then subsample the very high coverage amplucons (if there are any) it ought to work. I'll chase the colleague in case their code is available

afsanarupa commented 6 months ago

we have two fastq files for one sample as it is pair end sequence. We have targeted drug resistant genes, hsp65 gene and genes for spoligotyping sequences in this fastq files. with this hsp65 genes, can we detect species?

On Thu, May 9, 2024, 4:50 AM Zamin Iqbal @.***> wrote:

Apologies for missing this. I assume you mean targeted whete the targets are amplicons over AMR genes, as it done for m tuberculosis.

We looked into this recently with a colleague. Normally mykrobe will refuse to make predictions unless it can confirm the species first. You can force mykrobe to ignore the speciation step. But it still expects the same average depth across the whole genome . If you map your reads first, then subsample the very high coverage amplucons (if there are any) it ought to work. I'll chase the colleague in case their code is available

— Reply to this email directly, view it on GitHub https://github.com/Mykrobe-tools/mykrobe/issues/182#issuecomment-2101626411, or unsubscribe https://github.com/notifications/unsubscribe-auth/A4FAANU7VMP67FG6OHFHFJDZBKT4DAVCNFSM6AAAAABHGUC57OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBRGYZDMNBRGE . You are receiving this because you authored the thread.Message ID: @.***>

Afsana

iqbal-lab commented 6 months ago

Hi, For staph and TB, Mykrobe has it's own predefined probes for identifying species, defined by comparing many genomes of different related species. It is not set up to allow you to create your own species-defining probes. But you can tell it to ignore that step, and just predict resistance